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CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Heather A. Carlson, Richard D. Smith, Kelly L. Damm-Ganamet, Jeanne A. Stuckey, Aqeel Ahmed, Maire A. Convery, Donald O. Somers, Michael Kranz, Patricia A. Elkins, Guanglei Cui, Catherine E. Peishoff, Millard H. Lambert (+1 others)
2016 Journal of Chemical Information and Modeling  
In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR.  ...  In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound.  ...  The CSAR Center is funded by the National Institute of General Medical Sciences (U01 GM086873).  ... 
doi:10.1021/acs.jcim.5b00523 pmid:27149958 pmcid:PMC5228621 fatcat:5kin36kdjrfndps4w3yhge3tla

Protein–Ligand Scoring with Convolutional Neural Networks

Matthew Ragoza, Joshua Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes
2017 Journal of Chemical Information and Modeling  
Structure-based drug design methods rely on scoring functions to rank and predict binding affinities and poses.  ...  Scoring functions rank and score protein-ligand structures with the intertwined goals of accurately predicting the binding affinity of the complex, selecting the correct binding mode (pose prediction),  ...  under Grant DBI-1263020 and is co-funded by the Department of Defense.  ... 
doi:10.1021/acs.jcim.6b00740 pmid:28368587 pmcid:PMC5479431 fatcat:ws7v7a5k75dgzdf5l2octxpxb4

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

Sergei Grudinin, Maria Kadukova, Andreas Eisenbarth, Simon Marillet, Frédéric Cazals
2016 Journal of Computer-Aided Molecular Design  
Our pose predictions were ranked 3-9 for the HSP90 dataset, depending on the assessment metric.  ...  The main success of our pose prediction protocol was the re-scoring stage using the recently developed Convex-PL potential.  ...  Acknowledgments The authors thank Dr. Petr Popov from MIPT Moscow for the initial analysis of the HSP90 targets.  ... 
doi:10.1007/s10822-016-9976-2 pmid:27718029 fatcat:ofyasi7lzbbazl66nyh4e22jku

Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations

Ludovic Chaput, Edithe Selwa, Eddy Elisée, Bogdan I. Iorga
2018 Journal of Computer-Aided Molecular Design  
significant improvement in the ranking prediction compared with the direct ranking obtained from the scoring function.  ...  functional information available in public databases (PDB, ChEMBL, PubChem Assay, BindingDB, etc.); (ii) the docking of ligand dataset to provide a prediction for the binding modes and ranking of ligands  ...  This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LER-MIT) (Agence Nationale de la Recherche, Grant Number ANR-10-LABX-33), by the JPIAMR transnational  ... 
doi:10.1007/s10822-018-0161-7 pmid:30206740 fatcat:6pp7u2pk75gutnej5njlnyvm5e

Key Topics in Molecular Docking for Drug Design

Pedro H. M. Torres, Ana C. R. Sodero, Paula Jofily, Floriano P. Silva-Jr
2019 International Journal of Molecular Sciences  
the full potential of this area.  ...  their advantages and caveats, (ii) the advances in consensus methods, (iii) recent algorithms and applications using fragment-based approaches, and (iv) the use of machine learning algorithms in molecular  ...  Benchmarking Sets for Pose Prediction and Binding Affinity Calculations The development of either empirical parametric or nonparametric regression models for docking pose and binding affinity predictions  ... 
doi:10.3390/ijms20184574 pmid:31540192 pmcid:PMC6769580 fatcat:ye5rdnonofc3jjaizbncrdx2yu

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
2019 Journal of Computer-Aided Molecular Design  
to predict the binding modes and ranking of ligands.  ...  step the selection of the most suitable docking software for the system of interest based on structural and functional information available in public databases, followed by the docking of the dataset  ...  In the second step, we use these parameters for the prediction of binding modes (pose prediction) and of relative affinities of ligands (scoring).  ... 
doi:10.1007/s10822-019-00232-w pmid:31677003 fatcat:h57locrhsnbg3o7cyivy73auee

Protein flexibility in docking and surface mapping

Katrina W. Lexa, Heather A. Carlson
2012 Quarterly Reviews of Biophysics (print)  
These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%.  ...  As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state.  ...  Acknowledgments This work has been supported by the National Institutes of Health (GM65372).  ... 
doi:10.1017/s0033583512000066 pmid:22569329 pmcid:PMC4272345 fatcat:s7voxcdb7zbyrgkt7kedvo3lky

Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors

Damian Bartuzi, Agnieszka Kaczor, Katarzyna Targowska-Duda, Dariusz Matosiuk
2017 Molecules  
GPCRs are responsible for a vast part of signaling in vertebrates and, as such, invariably remain in the spotlight of medicinal chemistry.  ...  The growing number of studies on G protein-coupled receptors (GPCRs) family are a source of noticeable improvement in our understanding of the functioning of these proteins.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules22020340 pmid:28241450 fatcat:xyytfxpfcvd43dyoefto4qr5pi

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches

Alexander Tropsha, Nikolay V. Dokholyan, Eugene Muratov, Feng Ding, Denis Fourches
Selected models were used to predict the binding affinity of CSAR compounds towards the corresponding targets and rank them accordingly; the overall ranking accuracy evaluated by Spearman correlation was  ...  In parallel, MedusaDock designed to predict reliable docking poses was also used for ranking the CSAR ligands according to their docking scores; the resulting accuracy (Spearman correlation) for UK, ERK2  ...  The authors also acknowledge the financial support of NIH (grant GM66940 to A.T. and R01GM080742 to N.V.D.) and EPA (RD 83382501 and R832720).  ... 
doi:10.17615/733t-6r44 fatcat:qhylwywznzcm7l2en2elrc4dra

A multidisciplinary study of 3-(β- d -glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors

Sándor Kun, Jaida Begum, Efthimios Kyriakis, Evgenia C.V. Stamati, Thomas A. Barkas, Eszter Szennyes, Éva Bokor, Katalin E. Szabó, George A. Stravodimos, Ádám Sipos, Tibor Docsa, Pál Gergely (+8 others)
2018 European Journal of Medicinal Chemistry  
Accordingly, in silico screening of 2335 new analogues exploiting the ZINC docking database was performed and nine predicted candidates selected for synthesis.  ...  Chem. 2014, 76, 567).  ...  Post-docking minimization of the ligand poses was performed (with strain correction) and a maximum of 3 poses per ligand saved. Poses were ranked by 'docking score'.  ... 
doi:10.1016/j.ejmech.2018.01.095 pmid:29453094 fatcat:3kr4ieyakrbq5k6aodeoy2lc2m

Referee report. For: A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 2 approved with reservations]

Roland L. Dunbrack
.: D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2018; 32(1): 1-20.  ...  Lensink MF, Wodak SJ: Docking, scoring, and affinity prediction in CAPRI. Proteins. 2013; 81(12): 2082-95. PubMed Abstract | Publisher Full Text 30.  ...  like the PDB from the National Institutes of Health and the National Science Foundation.  ... 
doi:10.5256/f1000research.22602.r63141 fatcat:65v2v46cgbggzlbxfrq2gagjae

Measuring psychotic depression

S. D. Østergaard, B. S. Meyers, A. J. Flint, B. H. Mulsant, E. M. Whyte, C. M. Ulbricht, P. Bech, A. J. Rothschild
2013 Acta Psychiatrica Scandinavica  
Using the Danish National Registry of Patients, we identified all inpatient and outpatient diagnoses of VTE.  ...  Children with parents free of IBD were the comparison cohort.  ...  Fractional biliary excretion was calculated as the ratio between 11 C-CSar excreted into bile and 11 C-CSar supplied to the liver.  ... 
doi:10.1111/acps.12165 pmid:23799875 pmcid:PMC3819398 fatcat:laus7nv3kjdmhb54qwmigtuk2u

Understanding the Structure, Toxicity and Inhibition of IAPP at the Nanoscale

to the targeting of a range of amyloid diseases.  ...  Aggregation of human islet amyloid polypeptide (IAPP) to form amyloid fibrils and plaques is implicated in the dysfunction and death of pancreatic beta cells in type 2 diabetes, a most common form of metabolic  ...  The predictive power of MedusaScore has been validated in various benchmark studies, including recent community structure−activity resource (CSAR) blind ligand−receptor docking prediction exercises. 43  ... 
doi:10.26180/5ed4b0925ff3e fatcat:jzrcoxhcgzg7hfep6dnifu2dsu